#include "common.h"
#include "KmerHash.h"
#include "aligner.h"
#include <iostream>
#include <cstdlib>

using namespace std;

int main (int argc, char* argv[]) {
	if (argc != 4){
		cerr << "bin KmerLength chrNum HTName" << endl;
		return -1;
	}

	aligner_config = FAKE_ALIGN_BASE;

	_g_KmerLength = atoi(argv[1]);
	int chrNum = atoi(argv[2]);
	string HTName = argv[3];

	if (_g_KmerLength >= HASH_LEVEL * HASH_LENGTH) {
		cerr << "KmerLength too large" << endl;
		return -1;
	}

	aligner aligner_obj("human_g1k_v37.fasta", "read_180", HTName);

	aligner_obj.loadHT(chrNum);
	aligner_obj.alignChr(chrNum);
	aligner_obj.printStat();
	return 0;
}
